kay.gottschalk at weizmann.ac.il
Fri Jun 20 11:08:01 CEST 2003
my system is a protein with ATP, and I'm using the Gromacs ff. In the
initial pdb-file, 3 hydrogens are missing, thus Gromacs nicely
complains about that. If I just leave them out (with the '-missing'
option), ATP is too negatively charged. Is there any reasonable way to
build the hydrogens with Gromacs? Unfortunately I don't have Insight
here, and SwissPDB cannot do it. Alternatively I might increase the
radius and weight and decrease the charge of the affected oxygens in
the sense of a 'united atoms ATP', but I'd rather avoid that (the
dipoles just would be fucked up, and h-bonds will not be able to
form... ). Help would be appreciated.
Thanks a lot,
More information about the gromacs.org_gmx-users